DNA reveals prehistoric surprise

Click for interactive: Skulls of early Homo sapiens (right) and a Neanderthal (left, in background) sit at the Smithsonian's National Museum of Natural History. Scientists say a third hominin group may have co-existed with those two groups 40,000 years ago. Click on the image to learn more about human evolution, in the past and perhaps in the future.

A DNA sample taken from an ancient pinky bone suggests that a previously unknown group of human ancestors mixed it up with Neanderthals and modern humans 40,000 years ago. Was it a completely different species? Too early to say, but it might depend on what your definition of "species" is.

The finding, published in this week's issue of the journal Nature, emerged from a check of DNA samples from Denisova Cave in southern Siberia's Altai Mountains. Anthropologists know that the cave was occupied by human ancestors off and on for at least 125,000 years, based on the artifacts and bits of bone found there.

The pinky bone was found in 2008, within a layer of material that has been dated to between 30,000 and 48,000 years ago. That's the precise time frame when both modern humans and Neanderthals inhabited the Altai Mountains. So when Johannes Krause of Germany's Max Planck Institute for Evolutionary Anthropology and his colleagues analyzed the mitochondrial DNA from the pinky bone, they expected the genetic code to match up with one species or the other.

Krause was surprised to discover that it didn't match either species. A colleague of his at the institute, Svante Pääbo, was even more surprised when Krause told him about it.

"At first I really didn't believe him," Pääbo, one of the world's top experts on ancient DNA analysis, told reporters during a teleconference. "I thought he was pulling my leg."

Riddles within riddlesThe DNA posed an intriguing riddle: Mitochondrial DNA comes from the cellular energy factories outside the nucleus, and is passed down from a mother to her children. It can't provide the detailed genetic signature you can get from nuclear DNA. But it can serve as a "molecular clock" for evolutionary change, because it appears to mutate at a steady rate over time. Scientists can compare two different strings of mitochondrial coding to estimate when the two different organisms diverged on the evolutionary family tree.

The researchers ran the numbers for the pinky-bone sample, which they presume came from a young female nicknamed "X-Woman." They concluded that X-Woman's ancestors diverged from modern humans and Neanderthals about 1 million years ago. And that conclusion raised another riddle.

Based on previous research, anthropologists have thought that there were three great migrations of human ancestors out of Africa: The first came 1.9 million years ago, when Homo erectus headed toward Asia. The second came 300,000 to 500,000 years ago, when the ancestors of the Neanderthals trekked toward Europe and western Asia. The third occurred just 50,000 to 70,000 years ago, when anatomically modern humans headed out of Africa.

The fact that X-Woman's mitochondrial DNA was distinct from that of Neanderthals or modern humans would suggest that a third group of now-extinct human ancestors was still living in Siberia 40,000 years ago. Were they an offshoot from a completely different wave of migrants who left Africa after Homo erectus but before the ancestors of the Neanderthals? A different species entirely? The researchers are withholding judgment until they can sequence X-Woman's nuclear DNA. Pääbo said the results could be available "rather soon" but declined to give a precise timetable.

The species question is complicated because the various groups of human ancestors, known as hominins, might have interbred. That may go against one of the standard definitions of a species, as a group that can breed only amongst themselves. But evolutionary biologists are finding that nature doesn't necessarily obey our standard definitions. Neanderthals, for example, may have interbred with humans at some point. The same situation may apply to X-Woman.

"If it's just a modern human [that has] funny mitochondrial DNA, then you wouldn't call it a new species," Krause observed. Pääbo said he was "a bit skeptical about the fact that we can always have a clear species definition."

Migrants meeting migrantsAlthough they're cautious about the species question, Pääbo and Krause are confident that X-Woman represents a distinct group of migrants out of Africa. The "Hobbit" fossils found in Indonesia, which have been designated Homo floresiensis, apparently represent another. This is leading researchers to wonder whether human ancestors used the out-of-Africa route over and over again.

"Maybe it's an oversimplification to think about particular migrations out of Africa - saying there was one 2 million years ago, one half a million years ago, one 50,000 years ago. There might have been more or less continuous gene flow or migration that now and again is more frequent, less frequent," Pääbo said. "The picture that's going to emerge in the next years might be a more complex one."

In a commentary also published by Nature, the University of Manchester's Terence Brown said the mere fact that the research team was able to analyze 40,000-year-old DNA from X-Woman's pinky bone was an amazing achievement.

"The demonstration that a bone fragment can provide evidence for an unknown hominin will surely prompt more studies of this kind," he wrote, "and, possibly, increase the crowd of ancestors that early modern humans met when they traveled into Eurasia."

There may be more X-Women and X-Men out there, just waiting to be discovered. "After this amazing shock to find this, I would not be the one to say that one will not find new surprising things," Pääbo said.

Update for 2:45 p.m. ET March 25: There's quite a bit of buzz about all this among anthropologists - mostly on the question of whether or not X-Woman represents a new hominin species. ("Hominin" is currently the "in" term for humans and their extinct ancestors, and some would even classify chimps and bonobos as hominins as well. X-Woman is the nickname for the individual behind the pinky bone found in Siberia, even though the researchers don't yet know ... or at least haven't said ... whether that individual was female or male.)

A successful analysis of X-Woman's nuclear DNA would show how genetically distinct that creature was from modern humans and Neanderthals. If the genome is significantly different, that would strengthen the case for using a new species label. But the species identification would be something completely different from the usual routine, since it would be based on genetics alone.

Eventually, you'd want to link up the genetic identification with a morphological identification - that is, a set of bones that have a characteristic look to them. This would mean finding enough bones to identify, and then getting a DNA sequence that's sufficiently similar to X-Woman's. Only then could anyone say with confidence whether X-Woman belonged to some sort of Homo erectus offshoot, or a different species that we already know about (Heidelbergensis? Antecessor?), or a species that was previously unknown.

Anthropologists might eventually have to come up with a new way of identifying extinct hominin genomes, with a nomenclature that doesn't necessarily go by species names. For example, you could have Type 1 (Homo sapiens), Types 2 through 4 (Homo neanderthalensis), Type 5 (Homo floresiensis), Type 6 (X-Woman) and so on. In any case, it could take a long time to mesh the old, bone-based classification system with new genetic technologies.

The researchers behind the Nature study include Johannes Krause, Qiaomei Fu, Bence Viola and Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany; Jeffrey M. Good of the University of Montana in Missoula; and Michael V. Shunkov and Anatoli P. Derevianko of the Russian Academy of Sciences, Siberian Branch.